Instead of two days of talks, Bush and al-Maliki will have breakfast and a single meeting followed by a news conference on Thursday morning, the White House said.
The meeting will focus on the reposition of U.S. troops inside Iraq, engaging Iran and Syria, and dealing with militias, reports CBS News chief White House correspondent Jim Axelrod.
Bush and al-Maliki are also expected to agree on the transfer of more authority to Iraqi security forces, said U.S. Ambassador to Iraq Zalmay Khalilzad.
"There will be an agreement on transfer of capabilities, Iraqi capabilities at the faster rate to the Iraqis and to the prime minister, yes," he told CBS Evening News anchor Katie Couric.
The abrupt cancellation was an almost unheard-of development in the high-level diplomatic circles of a U.S. president, a king and a prime minister. There was confusion — and conflicting explanations —about what happened.
Bush had been scheduled to meet in a three-way session with al-Maliki and Jordan's King Abdullah II on Wednesday night. He and had rearranged his schedule to be in Amman for both days for talks aimed at reducing the spiral of violence in Iraq.
The last-minute cancellation was not announced until Bush had already come to Raghadan Palace and posed for photographs alone with the king.
White House counselor Dan Bartlett denied that the delay was a snub by al-Maliki directed at Bush or was related to the leak of a memo written by White House National Security Adviser Stephen Hadley questioning the prime minister's capacity for controlling violence in Iraq.
"Absolutely not," Bartlett said, adding that king and the prime minister had met before Mr. Bush arrived from a NATO summit in Latvia. "That negated the purpose to meet tonight together in a trilateral setting."
A senior administration official, who spoke with Khalilzad, basically echoed Bartlett's account.
The Jordanians and the Iraqis jointly decided it was not the best use of time because they both would be seeing the president separately, said the official.
Members of the Jordanian and Iraqi delegations contacted Khalilzad, who called Air Force One and spoke with Mr. Bush and Secretary of State Condoleezza Rice, giving them a heads-up, the official said.
However, Redha Jawad Taqi, a senior aide of top Shiite politician Abdul-Aziz al-Hakim who also was in Amman, said the Iraqis balked at the three-way meeting after learning the king wanted to broaden the talks to include the Israeli-Palestinian conflict.
Two senior officials traveling with al-Maliki, who spoke on condition of anonymity because of the sensitivity of the information, said the prime minister had been reluctant to travel to Jordan in the first place and decided, once in Amman, that he did not want "a third party" involved in talks about subjects specific to the U.S.-Iraqi relationship.
With al-Maliki already gone from the palace, Bush had an abbreviated meeting and dinner with the king before heading early to his hotel.
The cancellation came after the disclosure of a classified White House memo, written Nov. 8 by Hadley. In one particularly harsh section, Hadley asserted: "The reality on the streets of Baghdad suggests Maliki is either ignorant of what is going on, misrepresenting his intentions or that his capabilities are not yet sufficient to turn his good intentions into action."
Administration officials did not dispute the leaked account, saying that on balance the document was supportive of the Iraqi leader and generally portrayed him as well-meaning.
The president "has confidence in Prime Minister Maliki," said White House press secretary Tony Snow, who added that al-Maliki "has been very aggressive in recent weeks in taking on some of the key challenges."
The memo recommended steps to strengthen the Iraqi leader's position, including possibly sending more troops to defend Baghdad and providing monetary support for moderate political candidates for Iraq's parliament.
The Iraqi prime minister also faced political pressure at home about the summit. Thirty Iraqi lawmakers and five cabinet ministers loyal to anti-American cleric Muqtada al-Sadr said they were boycotting Parliament and the government to protest al-Maliki's presence at the summit.